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secr (version 1.4.0)

Spatially explicit capture-recapture

Description

Estimate animal population density with capture--recapture data from an array of passive detectors (traps). Models incorporating distance-dependent detection are fitted by maximizing the likelihood. Tools are included for data manipulation and model selection.

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Version

Install

install.packages('secr')

Monthly Downloads

7,107

Version

1.4.0

License

GPL (>= 2)

Maintainer

Murray Efford

Last Published

May 7th, 2010

Functions in secr (1.4.0)

print.traps

Print Detectors
AIC.secr

Compare SECR Models
flip.traps

Flip Detector Array
score.test

Score Test for SECR Models
rbind.capthist

Combine capthist Objects
secr.make.newdata

Create Default Design Data
session

Session Vector
sim.popn

Simulate 2-D Population
secr.model.density

Density Models
capthist.parts

Dissect Spatial Capture History Object
confint.secr

Profile Likelihood Confidence Intervals
coef.secr

Coefficients of secr Object
deviance

Deviance of fitted secr model and residual degrees of freedom
print.secr

Print secr Object
read.traps

Read Detector Data From File
covariates

Covariates Attribute
stoatDNA

Stoat DNA data
subset.mask

Subset Mask Object
skink

Skink Pitfall Data
closure.test

Closure tests
ip.secr

Spatially Explicit Capture--Recapture by Inverse Prediction
read.capthist

Import or export data
secr.model.detection

Models for Detection Parameters
pdot

Net Detection Probability
LR.test

Likelihood Ratio Test for SECR Models
deermouse

Deermouse Live-trapping Datasets
derived

Derived Parameters of Fitted SECR Model
popn

Population Object
reduce.capthist

Combine Occasions
shift.traps

Shift Detectors
subset.traps

Subset traps Object
homerange

Home Range Statistics
secr-package

Spatially Explicit Capture--Recapture Models
logmultinom

Multinomial Coefficient of SECR Likelihood
distancetotrap

Distance To Nearest Detector
ovensong

Ovenbird Acoustic Dataset
print.mask

Print Habitat Mask
plot.mask

Plot Habitat Mask
plot.secr

Plot Detection Functions
secrdemo

SECR Models Fitted to Demonstration Data
plot.capthist

Plot Detection Histories
capthist

Spatial Capture History Object
closedN

Closed population estimates
predict.secr

SECR Model Predictions
detectfn

Detection Functions
flip

Flip Points
rbind.popn

Combine popn Objects
make.mask

Build Habitat Mask
model.average

Model averaging for SECR Models
vcov.secr

Variance - Covariance Matrix of SECR Parameters
possum

Brushtail Possum Trapping Dataset
rotate

Rotate Points
D.designdata

Construct Density Design Data
LLsurface.secr

Plot likelihood surface
logit

Logit Transformation
mask

Mask Object
make.capthist

Construct capthist Object
rotate.traps

Rotate Detectors
autoini

Initial Parameter Values for SECR
housemouse

House mouse live trapping data
reduce

Combine Columns
verify

Check SECR Data
sim.secr

Simulate From Fitted secr Model
secr.design.MS

Construct Detection Model Design Matrices and Lookups
detector

Detector Type
make.traps

Build Detector Array
ellipse.secr

Confidence ellipse
traps.info

Detector Attributes
write.captures

Write Data to Text File
summary.traps

Summarise Detector Array
rbind.traps

Combine traps Objects
summary.capthist

Summarise Detections
secr.model

Spatially Explicit Capture--Recapture Models
FAQ

Frequently Asked Questions, And Others
secr.fit

Spatially Explicit Capture--Recapture
plot.traps

Plot traps Object
plot.popn

Plot popn Object
read.mask

Read Habitat Mask From File
print.capthist

Print Detections
sim.capthist

Simulate Detection Histories
summary.mask

Summarise Habitat Mask
trim

Drop Unwanted List Components
subset.capthist

Subset or Split capthist Object
traps

Detector Array
usage

Detector Usage
SPACECAP

Exchange data with SPACECAP package
ovenbird

Ovenbird Mist-netting Dataset
shift

Shift Points